The spot needed to hit to block regeneration is minuscule, right? What if Claire didn't actually hit that spot with her shard of glass? We know that normal regeneration is a little slower when it's healing severe injuries. And I think she and Angela left the room pretty soon afterwards. What if Sylar regenerated about a minute after they'd left. He would know the risk of Meredith exploding, so he'd evacuate himself pretty quickly. He could have just gone to the window and levitated himself out, and no one would have seen because they were all still indoors.